6. Density plots

suppressPackageStartupMessages({
  library("SummarizedExperiment")
  library("magrittr")
  library("plotlyutils")
  library("plotly")
  library("limma")
})

• TCGA Glioblastoma (GBM) data
• 5,000 randomly chosen genes, plus a gene signature (mentioned in vignette G)

mat <- assay(GBMdata) + 0.5
# ind <- sample(1:ncol(mat), 30)
plotly_density(
    log2(mat), 
    palette=colorspace::rainbow_hcl,
    xlab = "log<sub>2</sub>(reads + 0.5)") %>% 
    layout(showlegend = FALSE)

plotly_density(
    voomed_GBM$E, 
    palette=colorspace::rainbow_hcl,
    xlab = "log<sub>2</sub>(normalised counts per million)") %>%
    layout(showlegend = FALSE)